In the near future it is possible to instantaneously measure and quantify a person's state of mind and personality. This information is recorded and processed. The standard by which a persons' mind is referred to as the "Psycho-Pass".
Akane’s case deals with an insane man who has taken a woman hostage and raped her, holing himself up in a building inhabited by groups of the homeless. While Kogami is recuperating from Akane’s Paralyzer shot, she begins to worry about whether she is suited to be an Inspector after the fallout from her first case. On her second day on the job, she begins to learn more about the Enforcers she works with.
Ginoza and Akane, along with the Enforcers, are brought in to investigate a death caused by a Drone at a Drone manufacturing plant. When the Psycho-Pass of the entire staff checks out, they question whether it was an accident or possibly murder. When the CID is brought in to investigate a disappearance of Kimihiko Hayama, they discover that not only has he been killed, but someone has taken over his net avatar, Talisman. The CID tries to track down the fake Talisman in order to find the killer.
The CID’s hunt for Kimihiko Hayama’s killer leads them to another murder with the same modus operandi. Now it’s up to the CID to figure out how to track down the killer’s real identity and get justice for the victims.
After reading Kogami’s personnel file, Akane attempts to learn more about Kogami’s past and why he ended up as an Enforcer. Meanwhile, the CID detectives attempt to figure out who was helping Kanehara commit murders in the Hachioji Drone incident.
After realizing that the recent murders and the Specimen Case are indeed connected, Ginoza takes Kogami off the case and requests Tsunemori to watch over him. Tsunemori discusses Sasayama's murder with Kogami, and he gives her his one piece of evidence: a blurry image of Makishima.
With his profiling skills, Kogami determines that the girls' school killer isn't the same murderer from the unsolved case years ago; he explains that the recent murders lack "originality" and pointed social commentary of the previous killings.
Kogami, attempting to track down Makishima, takes Tsunemori to visit his former teacher, Jouji Saiga, who agrees to give her a crash course on criminal profiling; however, Ginoza reprimands her harshly which results into an argument.
Makishima and Senguji set up a hunt by using Tsunemori's friend Yuki as bait to lure Kogami into an abandoned subway station. Upon entering the station, Kogami discovers Yuki and loses contact with Tsunemori; the two must evade Senguji and his canine drones as a curious Makishima observes from above.
With a drone delivering him a Dominator, Kogami manages to outwit Senguji and kill him, although he also takes some shots in the process. Just then, Yuki is captured by Makishima, with Kogami too weak to follow. As Masaoka tends to Kogami's injuries, Tsunemori goes alone to pursue Makishima.
Taking place three years prior to the series, the episode focuses on Yayoi, who was a guitarist in a band before being imprisoned in a rehabilitation facility for being a latent criminal.
Ginoza meets up with the head of the Public Security Bureau about Makishima, who confidentially reveals to him about the real culprit of the Specimen Case, Touma Kouzoburou, three years ago who happens to be "criminally asymptomatic" just like Makishima.
As footage of the helmet killings appear on the internet, the helmets are distributed to more criminals who begin committing more horrendous crimes out in the open, prompting bloodthirsty revenge from the public in the name of self-defense. As the MWSPB are sent in to suppress the riots, Kogami deduces that the riots are intended to draw the police away from the Health and Welfare Ministry's Nona Tower facility, where the Sibyl System is located. As Makishima and his gang break in, Kogami, Akane and Shuusei head to the scene.
After Makishima is taken in and the riots are brought under control, Kogami remains curious about how Makishima will be judged, as well as the whereabouts of Shuusei. Later that day, Kasei tells Ginoza that Makishima's case has been taken out of the MWPSB's hands and orders him to investigate Shuusei's whereabouts, much to the ire of both Ginoza and Kogami. Later, Makishima is confronted by Kasei who reveals herself as Kouzoborou and shares a cybernetic body with Kasei. He explains to Makishima about the true nature of the Sybil System, which is revealed to be a supercomputer network comprised of human brains of criminally asymptomatic individuals like him. Kouzoborou offers Makishima to become a part of the System. But he refuses and instead kills Kouzaborou and escapes from the transit which is supposed to take him to the Ministry of Welfare before briefly contacting Kogami about his escape..
Ginoza, whose Hue is now problematic, eschews intensive therapy in order to work on retrieving Kogami and Makishima. He argues with Masaoka over his "softness," and declares his intention to see his "obsession" through to the end. Kogami, meanwhile, goes to visit Saiga in order to figure out Makishima's next move; the two surmise that Makishima might attempt to meddle with Japan's food supply in order to force open borders for the country. Shion does her best to comfort Akane and Kasei connects with Sibyl to determine their new "pawn." Later, a Dominator-bearing drone comes to visit Akane in the office - and declares that it will tell her the truth about everything.
As Makishima works on reprogramming the virus, both Kogami and the MWPSB arrive at the factory, with Kogami instructing Akane that they need to shut down power to the facility to bypass the security. Prior to arriving, Akane manages to convince the Sibyl System to keep her Dominator on Paralyzer mode with the safety unlocked regardless of Crime Coefficient to use as a trump card against Makishima and Kogami. After the power is shut down, Kogami sneaks into the facility whilst Akane and Yayoi head to the control room in case Makishima attempts to activate the emergency power. Finding the control room empty, Akane comes to realise that Ginoza and Masaoka are in danger. As Ginoza becomes trapped under a container after tripping up a trap, Masaoka comes face to face with Makishima. Although Masaoka appears to get the upper hand, Makishima threatens to blow Ginoza up with a stick of dynamite, with Masaoka ultimately sacrificing himself to save his son. As Ginoza remains horrified by his father's death, Kogami pursues Makishima and prepares to engage in a knife fight with him..
Due to the incredible success of the Sibyl System, Japan has begun exporting the technology to other countries with the hope that it will one day be used all around the world. In order to test its effectiveness in a foreign location, the war-torn state of the South East Asian Union (SEAUn) decides to implement the system, hoping to bring peace and stability to the town of Shambala Float and keep the population in check.